When you save a document that you have been editing, PDF Annotator adds your annotations to the PDF file, so that anyone using any PDF application such as Adobe Reader can see them.
To save the document that you have been editing in a new file, choose File Save as. If you want to save the existing file, choose File Save.
When you open the document again in PDF Annotator, you will normally be able to continue editing your comments. However, if the default option has been replaced by Persistence Mode, then all comments will be merged with the document before you save it.